Figure 120. Abundance. Data grouped by Sample.type,visit. bar_stacked plot. Image file: 
plots/323471e1474.svg. 
noone@mail.com Analysis of Dieting study 16S data % Fri Sep 7 05:46:18 2018
Plots are shown with relation to various combinations of meta data variables and in different graphical representations. Lots of plots here.
The same data are shown in multiple combinations of graphical representations. This is the same data, but each plot highlights slightly different aspects of it. It is not likely that you will need every plot - pick only what you need.
(1.1.1.3.3.2.2.2.1.1.0) Table 37. Data table used for plots. Data grouped by Sample.type,visit. Showing only 200 first rows. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.3.3.2.2.2.1.1.0-3237b5a8742.1.1.1.3.3.2.2.2.1.1.csv
| .record.id | Sample.type | visit | feature | Abundance |
|---|---|---|---|---|
| SM1 | patient | 1 | Bacteroides | 7.735e-01 |
| SM10 | patient | 3 | Bacteroides | 2.364e-01 |
| SM100 | patient | 4 | Bacteroides | 5.420e-01 |
| SM11 | patient | 2 | Bacteroides | 8.578e-01 |
| SM12 | patient | 1 | Bacteroides | 8.674e-01 |
| SM13 | patient | 1 | Bacteroides | 4.295e-01 |
| SM14 | patient | 1 | Bacteroides | 3.976e-02 |
| SM15 | control | 1 | Bacteroides | 4.120e-01 |
| SM16 | patient | 4 | Bacteroides | 3.890e-01 |
| SM17 | patient | 1 | Bacteroides | 8.130e-01 |
| SM18 | patient | 2 | Bacteroides | 6.537e-01 |
| SM19 | patient | 2 | Bacteroides | 2.221e-01 |
| SM2 | patient | 1 | Bacteroides | 8.611e-01 |
| SM20 | control | 1 | Bacteroides | 3.742e-01 |
| SM21 | patient | 1 | Bacteroides | 4.490e-01 |
| SM22 | patient | 1 | Bacteroides | 5.831e-01 |
| SM23 | patient | 2 | Bacteroides | 2.796e-01 |
| SM24 | patient | 1 | Bacteroides | 1.435e-01 |
| SM25 | patient | 4 | Bacteroides | 4.520e-01 |
| SM26 | control | 1 | Bacteroides | 5.242e-01 |
| SM28 | control | 1 | Bacteroides | 2.194e-01 |
| SM29 | patient | 3 | Bacteroides | 9.002e-01 |
| SM3 | patient | 2 | Bacteroides | 2.542e-01 |
| SM30 | patient | 4 | Bacteroides | 6.581e-02 |
| SM31 | control | 2 | Bacteroides | 4.094e-01 |
| SM33 | patient | 1 | Bacteroides | 1.747e-01 |
| SM35 | control | 1 | Bacteroides | 6.247e-01 |
| SM36 | patient | 4 | Bacteroides | 3.219e-04 |
| SM37 | control | 1 | Bacteroides | 3.301e-01 |
| SM38 | patient | 2 | Bacteroides | 9.828e-01 |
| SM39 | patient | 1 | Bacteroides | 4.095e-01 |
| SM40 | patient | 4 | Bacteroides | 6.908e-01 |
| SM41 | patient | 1 | Bacteroides | 5.037e-01 |
| SM42 | patient | 4 | Bacteroides | 6.901e-01 |
| SM43 | patient | 4 | Bacteroides | 6.589e-01 |
| SM44 | control | 1 | Bacteroides | 1.150e-02 |
| SM45 | patient | 2 | Bacteroides | 0.000e+00 |
| SM48 | control | 1 | Bacteroides | 3.247e-01 |
| SM49 | patient | 1 | Bacteroides | 9.292e-01 |
| SM5 | patient | 3 | Bacteroides | 5.313e-01 |
| SM50 | patient | 3 | Bacteroides | 0.000e+00 |
| SM51 | patient | 4 | Bacteroides | 7.122e-01 |
| SM52 | patient | 1 | Bacteroides | 8.105e-02 |
| SM53 | patient | 2 | Bacteroides | 3.305e-01 |
| SM54 | patient | 3 | Bacteroides | 6.239e-01 |
| SM55 | control | 1 | Bacteroides | 7.465e-02 |
| SM56 | patient | 2 | Bacteroides | 1.958e-02 |
| SM57 | patient | 1 | Bacteroides | 8.679e-01 |
| SM58 | patient | 2 | Bacteroides | 2.592e-02 |
| SM59 | patient | 3 | Bacteroides | 5.206e-02 |
| SM60 | patient | 3 | Bacteroides | 8.428e-01 |
| SM62 | patient | 1 | Bacteroides | 9.643e-01 |
| SM63 | control | 1 | Bacteroides | 5.135e-01 |
| SM64 | patient | 2 | Bacteroides | 6.977e-01 |
| SM65 | patient | 3 | Bacteroides | 3.711e-01 |
| SM66 | control | 1 | Bacteroides | 6.218e-01 |
| SM67 | patient | 4 | Bacteroides | 5.778e-01 |
| SM68 | patient | 4 | Bacteroides | 1.440e-01 |
| SM69 | patient | 4 | Bacteroides | 8.051e-01 |
| SM7 | control | 1 | Bacteroides | 2.126e-01 |
| SM70 | control | 1 | Bacteroides | 6.327e-02 |
| SM71 | patient | 3 | Bacteroides | 8.388e-01 |
| SM72 | control | 1 | Bacteroides | 4.762e-03 |
| SM73 | patient | 1 | Bacteroides | 8.108e-01 |
| SM74 | control | 2 | Bacteroides | 8.216e-02 |
| SM75 | patient | 3 | Bacteroides | 2.377e-03 |
| SM76 | control | 1 | Bacteroides | 8.153e-01 |
| SM77 | patient | 2 | Bacteroides | 7.039e-01 |
| SM79 | patient | 2 | Bacteroides | 1.173e-01 |
| SM8 | patient | 1 | Bacteroides | 7.723e-01 |
| SM81 | control | 1 | Bacteroides | 0.000e+00 |
| SM82 | patient | 4 | Bacteroides | 8.624e-01 |
| SM83 | patient | 1 | Bacteroides | 8.199e-01 |
| SM84 | patient | 1 | Bacteroides | 2.885e-01 |
| SM86 | patient | 2 | Bacteroides | 2.482e-03 |
| SM87 | patient | 1 | Bacteroides | 5.438e-01 |
| SM88 | patient | 2 | Bacteroides | 7.940e-01 |
| SM89 | control | 1 | Bacteroides | 2.115e-03 |
| SM9 | patient | 2 | Bacteroides | 6.096e-01 |
| SM90 | patient | 2 | Bacteroides | 4.088e-01 |
| SM91 | patient | 3 | Bacteroides | 6.525e-01 |
| SM92 | patient | 3 | Bacteroides | 7.921e-01 |
| SM93 | patient | 1 | Bacteroides | 6.404e-01 |
| SM95 | control | 1 | Bacteroides | 4.955e-01 |
| SM96 | patient | 1 | Bacteroides | 6.375e-01 |
| SM98 | patient | 3 | Bacteroides | 2.848e-01 |
| SM99 | patient | 3 | Bacteroides | 6.503e-01 |
| SM1 | patient | 1 | Prevotella | 2.598e-04 |
| SM10 | patient | 3 | Prevotella | 0.000e+00 |
| SM100 | patient | 4 | Prevotella | 7.692e-05 |
| SM11 | patient | 2 | Prevotella | 3.477e-04 |
| SM12 | patient | 1 | Prevotella | 1.328e-04 |
| SM13 | patient | 1 | Prevotella | 1.652e-02 |
| SM14 | patient | 1 | Prevotella | 1.855e-02 |
| SM15 | control | 1 | Prevotella | 1.415e-04 |
| SM16 | patient | 4 | Prevotella | 0.000e+00 |
| SM17 | patient | 1 | Prevotella | 4.137e-04 |
| SM18 | patient | 2 | Prevotella | 3.357e-04 |
| SM19 | patient | 2 | Prevotella | 2.314e-03 |
| SM2 | patient | 1 | Prevotella | 2.480e-04 |
| SM20 | control | 1 | Prevotella | 0.000e+00 |
| SM21 | patient | 1 | Prevotella | 0.000e+00 |
| SM22 | patient | 1 | Prevotella | 0.000e+00 |
| SM23 | patient | 2 | Prevotella | 0.000e+00 |
| SM24 | patient | 1 | Prevotella | 6.822e-01 |
| SM25 | patient | 4 | Prevotella | 0.000e+00 |
| SM26 | control | 1 | Prevotella | 2.758e-04 |
| SM28 | control | 1 | Prevotella | 3.997e-04 |
| SM29 | patient | 3 | Prevotella | 0.000e+00 |
| SM3 | patient | 2 | Prevotella | 4.458e-02 |
| SM30 | patient | 4 | Prevotella | 2.762e-03 |
| SM31 | control | 2 | Prevotella | 1.618e-03 |
| SM33 | patient | 1 | Prevotella | 0.000e+00 |
| SM35 | control | 1 | Prevotella | 2.046e-03 |
| SM36 | patient | 4 | Prevotella | 0.000e+00 |
| SM37 | control | 1 | Prevotella | 7.741e-04 |
| SM38 | patient | 2 | Prevotella | 1.028e-04 |
| SM39 | patient | 1 | Prevotella | 4.073e-01 |
| SM40 | patient | 4 | Prevotella | 2.775e-04 |
| SM41 | patient | 1 | Prevotella | 0.000e+00 |
| SM42 | patient | 4 | Prevotella | 4.994e-04 |
| SM43 | patient | 4 | Prevotella | 7.452e-05 |
| SM44 | control | 1 | Prevotella | 3.227e-01 |
| SM45 | patient | 2 | Prevotella | 0.000e+00 |
| SM48 | control | 1 | Prevotella | 2.151e-03 |
| SM49 | patient | 1 | Prevotella | 0.000e+00 |
| SM5 | patient | 3 | Prevotella | 5.950e-02 |
| SM50 | patient | 3 | Prevotella | 0.000e+00 |
| SM51 | patient | 4 | Prevotella | 2.231e-04 |
| SM52 | patient | 1 | Prevotella | 8.062e-03 |
| SM53 | patient | 2 | Prevotella | 4.611e-01 |
| SM54 | patient | 3 | Prevotella | 0.000e+00 |
| SM55 | control | 1 | Prevotella | 6.747e-01 |
| SM56 | patient | 2 | Prevotella | 0.000e+00 |
| SM57 | patient | 1 | Prevotella | 3.600e-04 |
| SM58 | patient | 2 | Prevotella | 6.582e-01 |
| SM59 | patient | 3 | Prevotella | 0.000e+00 |
| SM60 | patient | 3 | Prevotella | 3.404e-04 |
| SM62 | patient | 1 | Prevotella | 0.000e+00 |
| SM63 | control | 1 | Prevotella | 2.703e-03 |
| SM64 | patient | 2 | Prevotella | 1.113e-04 |
| SM65 | patient | 3 | Prevotella | 1.374e-04 |
| SM66 | control | 1 | Prevotella | 2.198e-04 |
| SM67 | patient | 4 | Prevotella | 0.000e+00 |
| SM68 | patient | 4 | Prevotella | 2.586e-02 |
| SM69 | patient | 4 | Prevotella | 3.108e-04 |
| SM7 | control | 1 | Prevotella | 0.000e+00 |
| SM70 | control | 1 | Prevotella | 4.438e-01 |
| SM71 | patient | 3 | Prevotella | 1.723e-03 |
| SM72 | control | 1 | Prevotella | 2.651e-01 |
| SM73 | patient | 1 | Prevotella | 1.009e-04 |
| SM74 | control | 2 | Prevotella | 6.547e-04 |
| SM75 | patient | 3 | Prevotella | 0.000e+00 |
| SM76 | control | 1 | Prevotella | 5.743e-05 |
| SM77 | patient | 2 | Prevotella | 1.127e-04 |
| SM79 | patient | 2 | Prevotella | 6.782e-01 |
| SM8 | patient | 1 | Prevotella | 7.416e-04 |
| SM81 | control | 1 | Prevotella | 0.000e+00 |
| SM82 | patient | 4 | Prevotella | 2.141e-04 |
| SM83 | patient | 1 | Prevotella | 0.000e+00 |
| SM84 | patient | 1 | Prevotella | 4.502e-01 |
| SM86 | patient | 2 | Prevotella | 3.103e-04 |
| SM87 | patient | 1 | Prevotella | 1.804e-01 |
| SM88 | patient | 2 | Prevotella | 1.705e-04 |
| SM89 | control | 1 | Prevotella | 8.603e-01 |
| SM9 | patient | 2 | Prevotella | 8.227e-04 |
| SM90 | patient | 2 | Prevotella | 5.776e-03 |
| SM91 | patient | 3 | Prevotella | 2.212e-04 |
| SM92 | patient | 3 | Prevotella | 9.411e-02 |
| SM93 | patient | 1 | Prevotella | 0.000e+00 |
| SM95 | control | 1 | Prevotella | 0.000e+00 |
| SM96 | patient | 1 | Prevotella | 0.000e+00 |
| SM98 | patient | 3 | Prevotella | 5.140e-01 |
| SM99 | patient | 3 | Prevotella | 4.757e-04 |
| SM1 | patient | 1 | Unclassified_Lachnospiraceae | 4.529e-02 |
| SM10 | patient | 3 | Unclassified_Lachnospiraceae | 2.607e-01 |
| SM100 | patient | 4 | Unclassified_Lachnospiraceae | 1.308e-01 |
| SM11 | patient | 2 | Unclassified_Lachnospiraceae | 4.404e-03 |
| SM12 | patient | 1 | Unclassified_Lachnospiraceae | 1.049e-02 |
| SM13 | patient | 1 | Unclassified_Lachnospiraceae | 1.116e-02 |
| SM14 | patient | 1 | Unclassified_Lachnospiraceae | 6.172e-02 |
| SM15 | control | 1 | Unclassified_Lachnospiraceae | 5.053e-02 |
| SM16 | patient | 4 | Unclassified_Lachnospiraceae | 1.583e-01 |
| SM17 | patient | 1 | Unclassified_Lachnospiraceae | 2.938e-02 |
| SM18 | patient | 2 | Unclassified_Lachnospiraceae | 5.271e-02 |
| SM19 | patient | 2 | Unclassified_Lachnospiraceae | 1.055e-01 |
| SM2 | patient | 1 | Unclassified_Lachnospiraceae | 1.097e-02 |
| SM20 | control | 1 | Unclassified_Lachnospiraceae | 2.256e-02 |
| SM21 | patient | 1 | Unclassified_Lachnospiraceae | 5.532e-02 |
| SM22 | patient | 1 | Unclassified_Lachnospiraceae | 1.113e-01 |
| SM23 | patient | 2 | Unclassified_Lachnospiraceae | 4.148e-04 |
| SM24 | patient | 1 | Unclassified_Lachnospiraceae | 1.402e-02 |
| SM25 | patient | 4 | Unclassified_Lachnospiraceae | 8.430e-02 |
| SM26 | control | 1 | Unclassified_Lachnospiraceae | 7.501e-02 |
| SM28 | control | 1 | Unclassified_Lachnospiraceae | 9.952e-02 |
| SM29 | patient | 3 | Unclassified_Lachnospiraceae | 1.128e-02 |
| SM3 | patient | 2 | Unclassified_Lachnospiraceae | 1.560e-01 |
| SM30 | patient | 4 | Unclassified_Lachnospiraceae | 3.297e-01 |
| SM31 | control | 2 | Unclassified_Lachnospiraceae | 1.294e-02 |
| SM33 | patient | 1 | Unclassified_Lachnospiraceae | 3.934e-03 |
(1.1.1.3.3.2.2.2.1.1.1) Widget 38. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Stacked Bar Chart. Data grouped by Sample.type,visit. Click to see HTML widget file in full window: ./1.1.1.3.3.2.2.2.1.1.1-323552a4c8Dynamic.Pivot.Table.html
(1.1.1.3.3.2.2.2.1.1.1) Widget 39. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Table Barchart. Data grouped by Sample.type,visit. Click to see HTML widget file in full window: ./1.1.1.3.3.2.2.2.1.1.1-32324020e98Dynamic.Pivot.Table.html
(1.1.1.3.3.2.2.2.1.1.1) Table 38. Summary table. Data grouped by Sample.type,visit. Showing only 200 first rows. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.3.3.2.2.2.1.1.1-3237a17f021.1.1.1.3.3.2.2.2.1.1.csv
| feature | Sample.type | visit | mean | sd | median | incidence |
|---|---|---|---|---|---|---|
| Bacteroides | control | 1 | 3.125e-01 | 0.2538464 | 3.274e-01 | 0.94444 |
| Bacteroides | control | 2 | 2.458e-01 | 0.2313828 | 2.458e-01 | 1.00000 |
| Bacteroides | patient | 1 | 5.828e-01 | 0.2873867 | 6.375e-01 | 1.00000 |
| Bacteroides | patient | 2 | 4.094e-01 | 0.3304484 | 3.305e-01 | 0.94118 |
| Bacteroides | patient | 3 | 4.842e-01 | 0.3242795 | 5.776e-01 | 0.92857 |
| Bacteroides | patient | 4 | 5.070e-01 | 0.2819563 | 5.778e-01 | 1.00000 |
| Prevotella | control | 1 | 1.431e-01 | 0.2654918 | 5.869e-04 | 0.77778 |
| Prevotella | control | 2 | 1.136e-03 | 0.0006813 | 1.136e-03 | 1.00000 |
| Prevotella | patient | 1 | 7.676e-02 | 0.1823681 | 2.480e-04 | 0.60870 |
| Prevotella | patient | 2 | 1.090e-01 | 0.2379624 | 3.357e-04 | 0.82353 |
| Prevotella | patient | 3 | 4.789e-02 | 0.1371393 | 1.793e-04 | 0.57143 |
| Prevotella | patient | 4 | 2.331e-03 | 0.0071093 | 2.141e-04 | 0.69231 |
| Unclassified_Lachnospiraceae | control | 1 | 6.389e-02 | 0.0412008 | 6.129e-02 | 1.00000 |
| Unclassified_Lachnospiraceae | control | 2 | 6.654e-02 | 0.0757919 | 6.654e-02 | 1.00000 |
| Unclassified_Lachnospiraceae | patient | 1 | 2.933e-02 | 0.0314771 | 1.135e-02 | 0.95652 |
| Unclassified_Lachnospiraceae | patient | 2 | 4.774e-02 | 0.0603731 | 2.660e-02 | 0.94118 |
| Unclassified_Lachnospiraceae | patient | 3 | 9.946e-02 | 0.1218097 | 4.278e-02 | 1.00000 |
| Unclassified_Lachnospiraceae | patient | 4 | 8.700e-02 | 0.0868167 | 5.327e-02 | 1.00000 |
| Faecalibacterium | control | 1 | 4.217e-02 | 0.0440054 | 3.575e-02 | 0.94444 |
| Faecalibacterium | control | 2 | 3.452e-02 | 0.0442349 | 3.452e-02 | 1.00000 |
| Faecalibacterium | patient | 1 | 2.729e-02 | 0.0297587 | 2.047e-02 | 0.95652 |
| Faecalibacterium | patient | 2 | 5.994e-02 | 0.1135543 | 1.526e-02 | 0.88235 |
| Faecalibacterium | patient | 3 | 3.536e-02 | 0.0397725 | 2.075e-02 | 1.00000 |
| Faecalibacterium | patient | 4 | 6.643e-02 | 0.0771098 | 3.868e-02 | 1.00000 |
| Lachnospiracea_incertae_sedis | control | 1 | 3.238e-02 | 0.0266386 | 2.788e-02 | 0.94444 |
| Lachnospiracea_incertae_sedis | control | 2 | 5.683e-02 | 0.0797987 | 5.683e-02 | 1.00000 |
| Lachnospiracea_incertae_sedis | patient | 1 | 1.017e-02 | 0.0113133 | 4.911e-03 | 0.91304 |
| Lachnospiracea_incertae_sedis | patient | 2 | 3.467e-02 | 0.0451511 | 1.592e-02 | 0.88235 |
| Lachnospiracea_incertae_sedis | patient | 3 | 5.461e-02 | 0.0741321 | 1.830e-02 | 0.92857 |
| Lachnospiracea_incertae_sedis | patient | 4 | 5.532e-02 | 0.0598858 | 5.855e-02 | 0.92308 |
| Parabacteroides | control | 1 | 8.828e-03 | 0.0080690 | 6.610e-03 | 0.94444 |
| Parabacteroides | control | 2 | 1.807e-02 | 0.0190712 | 1.807e-02 | 1.00000 |
| Parabacteroides | patient | 1 | 3.735e-02 | 0.1051873 | 2.651e-03 | 0.73913 |
| Parabacteroides | patient | 2 | 5.616e-02 | 0.1713182 | 8.295e-04 | 0.82353 |
| Parabacteroides | patient | 3 | 3.337e-02 | 0.0584943 | 4.370e-03 | 0.64286 |
| Parabacteroides | patient | 4 | 3.474e-02 | 0.0922398 | 2.231e-04 | 0.69231 |
| Alistipes | control | 1 | 4.359e-02 | 0.0743642 | 1.748e-02 | 0.77778 |
| Alistipes | control | 2 | 6.305e-02 | 0.0836085 | 6.305e-02 | 1.00000 |
| Alistipes | patient | 1 | 3.249e-02 | 0.0560977 | 9.784e-03 | 0.69565 |
| Alistipes | patient | 2 | 2.111e-02 | 0.0418863 | 0.000e+00 | 0.47059 |
| Alistipes | patient | 3 | 6.408e-03 | 0.0158919 | 0.000e+00 | 0.42857 |
| Alistipes | patient | 4 | 7.073e-03 | 0.0117754 | 8.319e-04 | 0.53846 |
| Blautia | control | 1 | 2.657e-02 | 0.0444930 | 1.644e-02 | 1.00000 |
| Blautia | control | 2 | 4.533e-02 | 0.0618126 | 4.533e-02 | 1.00000 |
| Blautia | patient | 1 | 1.235e-02 | 0.0164027 | 4.067e-03 | 0.95652 |
| Blautia | patient | 2 | 1.868e-02 | 0.0333637 | 3.861e-03 | 0.82353 |
| Blautia | patient | 3 | 2.365e-02 | 0.0274097 | 1.545e-02 | 1.00000 |
| Blautia | patient | 4 | 1.464e-02 | 0.0193524 | 6.334e-03 | 1.00000 |
| Ruminococcus | control | 1 | 5.576e-02 | 0.0872197 | 2.428e-02 | 0.94444 |
| Ruminococcus | control | 2 | 1.140e-01 | 0.1423975 | 1.140e-01 | 1.00000 |
| Ruminococcus | patient | 1 | 5.175e-03 | 0.0091511 | 1.893e-03 | 0.91304 |
| Ruminococcus | patient | 2 | 5.007e-03 | 0.0085975 | 1.510e-03 | 0.76471 |
| Ruminococcus | patient | 3 | 1.107e-02 | 0.0216317 | 2.787e-03 | 0.85714 |
| Ruminococcus | patient | 4 | 6.834e-03 | 0.0137693 | 1.988e-03 | 0.76923 |
| Unclassified_Clostridiales | control | 1 | 1.825e-02 | 0.0216929 | 1.279e-02 | 0.94444 |
| Unclassified_Clostridiales | control | 2 | 3.991e-02 | 0.0204012 | 3.991e-02 | 1.00000 |
| Unclassified_Clostridiales | patient | 1 | 1.119e-02 | 0.0142830 | 7.085e-03 | 1.00000 |
| Unclassified_Clostridiales | patient | 2 | 9.744e-03 | 0.0119547 | 6.365e-03 | 0.88235 |
| Unclassified_Clostridiales | patient | 3 | 3.047e-02 | 0.0653628 | 1.140e-02 | 1.00000 |
| Unclassified_Clostridiales | patient | 4 | 1.318e-02 | 0.0159711 | 6.475e-03 | 1.00000 |
| Lactobacillus | control | 1 | 1.522e-02 | 0.0641403 | 0.000e+00 | 0.27778 |
| Lactobacillus | control | 2 | 0.000e+00 | 0.0000000 | 0.000e+00 | 0.00000 |
| Lactobacillus | patient | 1 | 3.493e-04 | 0.0011589 | 0.000e+00 | 0.17391 |
| Lactobacillus | patient | 2 | 5.878e-02 | 0.2418040 | 0.000e+00 | 0.29412 |
| Lactobacillus | patient | 3 | 3.806e-04 | 0.0012664 | 0.000e+00 | 0.21429 |
| Lactobacillus | patient | 4 | 5.014e-04 | 0.0015281 | 0.000e+00 | 0.23077 |
| Unclassified_Ruminococcaceae | control | 1 | 3.224e-02 | 0.0335651 | 1.940e-02 | 0.94444 |
| Unclassified_Ruminococcaceae | control | 2 | 5.710e-02 | 0.0451079 | 5.710e-02 | 1.00000 |
| Unclassified_Ruminococcaceae | patient | 1 | 1.240e-02 | 0.0253701 | 6.698e-03 | 1.00000 |
| Unclassified_Ruminococcaceae | patient | 2 | 6.016e-03 | 0.0085811 | 2.816e-03 | 0.88235 |
| Unclassified_Ruminococcaceae | patient | 3 | 5.898e-03 | 0.0076353 | 3.294e-03 | 1.00000 |
| Unclassified_Ruminococcaceae | patient | 4 | 8.677e-03 | 0.0119062 | 2.538e-03 | 1.00000 |
| Roseburia | control | 1 | 9.054e-03 | 0.0069943 | 6.302e-03 | 1.00000 |
| Roseburia | control | 2 | 1.069e-02 | 0.0071054 | 1.069e-02 | 1.00000 |
| Roseburia | patient | 1 | 5.268e-03 | 0.0062277 | 2.966e-03 | 0.86957 |
| Roseburia | patient | 2 | 1.656e-02 | 0.0256221 | 4.243e-03 | 0.94118 |
| Roseburia | patient | 3 | 1.476e-02 | 0.0161405 | 1.115e-02 | 1.00000 |
| Roseburia | patient | 4 | 3.631e-02 | 0.0373736 | 2.288e-02 | 1.00000 |
| Clostridium_XI | control | 1 | 9.259e-03 | 0.0108630 | 6.425e-03 | 0.94444 |
| Clostridium_XI | control | 2 | 1.387e-02 | 0.0081666 | 1.387e-02 | 1.00000 |
| Clostridium_XI | patient | 1 | 1.741e-02 | 0.0457103 | 2.423e-03 | 0.82609 |
| Clostridium_XI | patient | 2 | 1.178e-02 | 0.0350550 | 1.438e-03 | 0.76471 |
| Clostridium_XI | patient | 3 | 6.773e-03 | 0.0091778 | 2.379e-03 | 0.92857 |
| Clostridium_XI | patient | 4 | 2.371e-02 | 0.0353583 | 7.158e-03 | 1.00000 |
| Enterococcus | control | 1 | 3.133e-03 | 0.0131693 | 0.000e+00 | 0.16667 |
| Enterococcus | control | 2 | 3.437e-03 | 0.0048606 | 3.437e-03 | 0.50000 |
| Enterococcus | patient | 1 | 3.391e-03 | 0.0149272 | 0.000e+00 | 0.34783 |
| Enterococcus | patient | 2 | 4.222e-02 | 0.1722129 | 0.000e+00 | 0.41176 |
| Enterococcus | patient | 3 | 2.815e-04 | 0.0005849 | 0.000e+00 | 0.28571 |
| Enterococcus | patient | 4 | 3.035e-04 | 0.0006924 | 0.000e+00 | 0.23077 |
| Erysipelotrichaceae_incertae_sedis | control | 1 | 1.177e-03 | 0.0016041 | 6.149e-04 | 0.77778 |
| Erysipelotrichaceae_incertae_sedis | control | 2 | 8.955e-04 | 0.0001223 | 8.955e-04 | 1.00000 |
| Erysipelotrichaceae_incertae_sedis | patient | 1 | 2.007e-02 | 0.0799902 | 1.212e-03 | 0.73913 |
| Erysipelotrichaceae_incertae_sedis | patient | 2 | 1.738e-03 | 0.0028560 | 4.125e-04 | 0.82353 |
| Erysipelotrichaceae_incertae_sedis | patient | 3 | 9.515e-03 | 0.0139050 | 2.854e-03 | 1.00000 |
| Erysipelotrichaceae_incertae_sedis | patient | 4 | 1.522e-02 | 0.0500792 | 9.325e-04 | 0.84615 |
| Megamonas | control | 1 | 1.856e-02 | 0.0528681 | 0.000e+00 | 0.16667 |
| Megamonas | control | 2 | 0.000e+00 | 0.0000000 | 0.000e+00 | 0.00000 |
| Megamonas | patient | 1 | 2.174e-03 | 0.0104047 | 0.000e+00 | 0.08696 |
| Megamonas | patient | 2 | 1.961e-02 | 0.0573116 | 0.000e+00 | 0.11765 |
| Megamonas | patient | 3 | 2.782e-03 | 0.0104102 | 0.000e+00 | 0.07143 |
| Megamonas | patient | 4 | 2.288e-03 | 0.0078271 | 0.000e+00 | 0.15385 |
| Sutterella | control | 1 | 1.005e-02 | 0.0274571 | 1.351e-03 | 0.61111 |
| Sutterella | control | 2 | 0.000e+00 | 0.0000000 | 0.000e+00 | 0.00000 |
| Sutterella | patient | 1 | 6.547e-03 | 0.0148652 | 4.426e-05 | 0.52174 |
| Sutterella | patient | 2 | 7.151e-03 | 0.0134897 | 0.000e+00 | 0.29412 |
| Sutterella | patient | 3 | 5.046e-03 | 0.0127503 | 0.000e+00 | 0.21429 |
| Sutterella | patient | 4 | 1.018e-02 | 0.0244892 | 0.000e+00 | 0.30769 |
| Escherichia_Shigella | control | 1 | 1.014e-02 | 0.0395132 | 3.219e-04 | 0.55556 |
| Escherichia_Shigella | control | 2 | 4.045e-04 | 0.0005721 | 4.045e-04 | 0.50000 |
| Escherichia_Shigella | patient | 1 | 1.410e-02 | 0.0440606 | 0.000e+00 | 0.39130 |
| Escherichia_Shigella | patient | 2 | 3.576e-04 | 0.0012975 | 0.000e+00 | 0.29412 |
| Escherichia_Shigella | patient | 3 | 2.356e-03 | 0.0051551 | 3.234e-04 | 0.64286 |
| Escherichia_Shigella | patient | 4 | 7.543e-03 | 0.0172863 | 8.323e-05 | 0.53846 |
| Unclassified_Bacteria | control | 1 | 1.364e-02 | 0.0114079 | 1.054e-02 | 1.00000 |
| Unclassified_Bacteria | control | 2 | 2.617e-02 | 0.0324305 | 2.617e-02 | 1.00000 |
| Unclassified_Bacteria | patient | 1 | 8.586e-03 | 0.0185047 | 3.658e-03 | 0.95652 |
| Unclassified_Bacteria | patient | 2 | 2.162e-03 | 0.0019168 | 1.958e-03 | 0.88235 |
| Unclassified_Bacteria | patient | 3 | 3.391e-03 | 0.0031220 | 2.417e-03 | 1.00000 |
| Unclassified_Bacteria | patient | 4 | 4.709e-03 | 0.0065490 | 1.415e-03 | 1.00000 |
| Clostridium_IV | control | 1 | 1.258e-02 | 0.0141985 | 5.803e-03 | 0.94444 |
| Clostridium_IV | control | 2 | 8.200e-02 | 0.0659652 | 8.200e-02 | 1.00000 |
| Clostridium_IV | patient | 1 | 5.157e-03 | 0.0087292 | 1.461e-03 | 0.82609 |
| Clostridium_IV | patient | 2 | 1.862e-03 | 0.0035789 | 2.569e-04 | 0.58824 |
| Clostridium_IV | patient | 3 | 1.834e-03 | 0.0036717 | 3.273e-04 | 0.64286 |
| Clostridium_IV | patient | 4 | 4.154e-03 | 0.0104238 | 3.219e-04 | 0.69231 |
| Clostridium_XlVa | control | 1 | 8.736e-03 | 0.0124426 | 4.491e-03 | 0.94444 |
| Clostridium_XlVa | control | 2 | 4.689e-03 | 0.0026269 | 4.689e-03 | 1.00000 |
| Clostridium_XlVa | patient | 1 | 6.183e-03 | 0.0072269 | 4.820e-03 | 0.95652 |
| Clostridium_XlVa | patient | 2 | 2.457e-03 | 0.0026715 | 1.468e-03 | 0.94118 |
| Clostridium_XlVa | patient | 3 | 1.005e-02 | 0.0164355 | 2.887e-03 | 1.00000 |
| Clostridium_XlVa | patient | 4 | 7.189e-03 | 0.0056921 | 6.764e-03 | 0.92308 |
| Unclassified_Firmicutes | control | 1 | 8.036e-03 | 0.0109414 | 3.210e-03 | 1.00000 |
| Unclassified_Firmicutes | control | 2 | 1.259e-02 | 0.0057974 | 1.259e-02 | 1.00000 |
| Unclassified_Firmicutes | patient | 1 | 2.429e-03 | 0.0033961 | 8.410e-04 | 0.86957 |
| Unclassified_Firmicutes | patient | 2 | 5.485e-03 | 0.0092386 | 7.794e-04 | 0.76471 |
| Unclassified_Firmicutes | patient | 3 | 9.325e-03 | 0.0180189 | 1.689e-03 | 1.00000 |
| Unclassified_Firmicutes | patient | 4 | 4.155e-03 | 0.0066088 | 9.688e-04 | 0.92308 |
| Haemophilus | control | 1 | 8.739e-04 | 0.0012254 | 2.922e-04 | 0.66667 |
| Haemophilus | control | 2 | 4.910e-03 | 0.0069438 | 4.910e-03 | 0.50000 |
| Haemophilus | patient | 1 | 5.492e-04 | 0.0016996 | 0.000e+00 | 0.34783 |
| Haemophilus | patient | 2 | 1.329e-03 | 0.0020544 | 1.127e-04 | 0.58824 |
| Haemophilus | patient | 3 | 6.978e-03 | 0.0142668 | 5.086e-04 | 0.50000 |
| Haemophilus | patient | 4 | 2.192e-02 | 0.0530352 | 2.236e-04 | 0.76923 |
| Bifidobacterium | control | 1 | 1.565e-02 | 0.0449947 | 1.592e-03 | 0.77778 |
| Bifidobacterium | control | 2 | 6.749e-03 | 0.0089723 | 6.749e-03 | 1.00000 |
| Bifidobacterium | patient | 1 | 1.791e-03 | 0.0046990 | 3.015e-04 | 0.65217 |
| Bifidobacterium | patient | 2 | 7.066e-04 | 0.0018786 | 5.138e-05 | 0.52941 |
| Bifidobacterium | patient | 3 | 3.665e-03 | 0.0070439 | 1.831e-04 | 0.57143 |
| Bifidobacterium | patient | 4 | 2.813e-03 | 0.0050442 | 2.231e-04 | 0.61538 |
| Dorea | control | 1 | 8.060e-03 | 0.0090249 | 4.976e-03 | 0.94444 |
| Dorea | control | 2 | 1.137e-02 | 0.0052122 | 1.137e-02 | 1.00000 |
| Dorea | patient | 1 | 4.921e-03 | 0.0096203 | 1.112e-03 | 0.73913 |
| Dorea | patient | 2 | 1.453e-03 | 0.0018565 | 8.393e-04 | 0.82353 |
| Dorea | patient | 3 | 6.028e-03 | 0.0104849 | 1.281e-03 | 0.85714 |
| Dorea | patient | 4 | 2.899e-03 | 0.0058484 | 6.232e-04 | 0.92308 |
| Unclassified_Bacteroidales | control | 1 | 2.201e-03 | 0.0039404 | 1.271e-03 | 0.83333 |
| Unclassified_Bacteroidales | control | 2 | 1.502e-03 | 0.0007359 | 1.502e-03 | 1.00000 |
| Unclassified_Bacteroidales | patient | 1 | 6.359e-03 | 0.0137559 | 2.017e-03 | 1.00000 |
| Unclassified_Bacteroidales | patient | 2 | 8.760e-03 | 0.0201346 | 1.942e-03 | 0.88235 |
| Unclassified_Bacteroidales | patient | 3 | 2.801e-03 | 0.0035044 | 2.015e-03 | 0.71429 |
| Unclassified_Bacteroidales | patient | 4 | 1.617e-03 | 0.0022822 | 5.550e-04 | 0.76923 |
| Clostridium_XVIII | control | 1 | 4.144e-03 | 0.0102711 | 1.151e-03 | 0.88889 |
| Clostridium_XVIII | control | 2 | 6.741e-03 | 0.0030526 | 6.741e-03 | 1.00000 |
| Clostridium_XVIII | patient | 1 | 3.581e-03 | 0.0042045 | 1.786e-03 | 0.86957 |
| Clostridium_XVIII | patient | 2 | 1.424e-03 | 0.0031420 | 4.636e-04 | 0.76471 |
| Clostridium_XVIII | patient | 3 | 6.793e-03 | 0.0151982 | 8.433e-04 | 0.78571 |
| Clostridium_XVIII | patient | 4 | 6.920e-03 | 0.0169633 | 1.387e-03 | 0.92308 |
| Akkermansia | control | 1 | 2.550e-03 | 0.0051198 | 0.000e+00 | 0.38889 |
| Akkermansia | control | 2 | 2.136e-02 | 0.0292859 | 2.136e-02 | 1.00000 |
| Akkermansia | patient | 1 | 1.056e-02 | 0.0368541 | 0.000e+00 | 0.34783 |
| Akkermansia | patient | 2 | 3.903e-04 | 0.0011122 | 0.000e+00 | 0.11765 |
| Akkermansia | patient | 3 | 5.727e-04 | 0.0018438 | 0.000e+00 | 0.14286 |
| Akkermansia | patient | 4 | 2.846e-05 | 0.0001026 | 0.000e+00 | 0.07692 |
| Veillonella | control | 1 | 1.392e-03 | 0.0051949 | 0.000e+00 | 0.33333 |
| Veillonella | control | 2 | 4.910e-04 | 0.0006944 | 4.910e-04 | 0.50000 |
| Veillonella | patient | 1 | 1.094e-03 | 0.0036140 | 0.000e+00 | 0.47826 |
| Veillonella | patient | 2 | 6.980e-03 | 0.0192133 | 1.957e-04 | 0.64706 |
| Veillonella | patient | 3 | 7.884e-03 | 0.0225365 | 4.661e-04 | 0.64286 |
| Veillonella | patient | 4 | 1.499e-03 | 0.0029191 | 1.554e-04 | 0.69231 |
| Streptococcus | control | 1 | 5.433e-03 | 0.0178726 | 3.570e-04 | 0.77778 |
| Streptococcus | control | 2 | 1.541e-03 | 0.0012534 | 1.541e-03 | 1.00000 |
| Streptococcus | patient | 1 | 2.134e-03 | 0.0048585 | 1.009e-04 | 0.69565 |
| Streptococcus | patient | 2 | 1.752e-03 | 0.0031860 | 2.816e-04 | 0.70588 |
| Streptococcus | patient | 3 | 5.250e-03 | 0.0163790 | 3.668e-04 | 0.71429 |
| Streptococcus | patient | 4 | 1.655e-03 | 0.0028281 | 3.077e-04 | 0.92308 |
| Clostridium_sensu_stricto | control | 1 | 3.142e-03 | 0.0073249 | 2.614e-04 | 0.72222 |
| Clostridium_sensu_stricto | control | 2 | 3.303e-03 | 0.0018102 | 3.303e-03 | 1.00000 |
| Clostridium_sensu_stricto | patient | 1 | 3.344e-03 | 0.0072111 | 6.071e-05 | 0.52174 |
| Clostridium_sensu_stricto | patient | 2 | 1.329e-03 | 0.0047976 | 0.000e+00 | 0.35294 |
| Clostridium_sensu_stricto | patient | 3 | 5.140e-03 | 0.0111072 | 9.659e-04 | 0.64286 |
| Clostridium_sensu_stricto | patient | 4 | 2.817e-03 | 0.0044321 | 5.550e-04 | 0.61538 |
| Unclassified_Clostridiaceae_1 | control | 1 | 5.124e-04 | 0.0013443 | 2.871e-05 | 0.50000 |
| Unclassified_Clostridiaceae_1 | control | 2 | 1.830e-03 | 0.0002729 | 1.830e-03 | 1.00000 |
| Unclassified_Clostridiaceae_1 | patient | 1 | 2.751e-04 | 0.0006520 | 0.000e+00 | 0.34783 |
| Unclassified_Clostridiaceae_1 | patient | 2 | 5.875e-04 | 0.0021706 | 0.000e+00 | 0.35294 |
| Unclassified_Clostridiaceae_1 | patient | 3 | 1.194e-02 | 0.0340117 | 5.139e-04 | 0.57143 |
| Unclassified_Clostridiaceae_1 | patient | 4 | 3.902e-03 | 0.0118332 | 1.554e-04 | 0.53846 |
| Klebsiella | control | 1 | 5.130e-03 | 0.0215002 | 0.000e+00 | 0.16667 |
| Klebsiella | control | 2 | 0.000e+00 | 0.0000000 | 0.000e+00 | 0.00000 |
(1.1.1.3.3.2.2.2.1.1.1) Figure 120. Abundance. Data grouped by Sample.type,visit. bar_stacked plot. Image file: plots/323471e1474.svg.
(1.1.1.3.3.2.2.2.1.1.1) Figure 121. Abundance. Data grouped by Sample.type,visit. bar (sample mean) plot. Image file: plots/323a72514d.svg. 
(1.1.1.3.3.2.2.2.1.1.1) Figure 122. Abundance. Data grouped by Sample.type,visit. violin plot. Image file: plots/3237bf6fa0f.svg. 
(1.1.1.3.3.2.2.2.1.1.1) Figure 123. Abundance. Data grouped by Sample.type,visit. boxplot plot. Image file: plots/32317dffe9e.svg. 
(1.1.1.3.3.2.2.2.1.2.1) Figure 124. Abundance. Data grouped by Sample.type,visit. bar (sample mean) plot. Image file: plots/323407ddd9c.svg. 
(1.1.1.3.3.2.2.2.1.2.1) Figure 125. Abundance. Data grouped by Sample.type,visit. violin plot. Image file: plots/323182452f9.svg. 
(1.1.1.3.3.2.2.2.1.2.1) Figure 126. Abundance. Data grouped by Sample.type,visit. boxplot plot. Image file: plots/32328458021.svg. 
(1.1.1.3.3.2.2.2.2.1.1) Figure 127. Abundance. Data grouped by Sample.type,visit. bar (sample mean) plot. Image file: plots/32318ea7169.svg. 
(1.1.1.3.3.2.2.2.2.1.1) Figure 128. Abundance. Data grouped by Sample.type,visit. violin plot. Image file: plots/3232e9cd17.svg. 
(1.1.1.3.3.2.2.2.2.1.1) Figure 129. Abundance. Data grouped by Sample.type,visit. boxplot plot. Image file: plots/323424673bc.svg. 
(1.1.1.3.3.2.2.2.2.2.1) Figure 130. Abundance. Data grouped by Sample.type,visit. bar (sample mean) plot. Image file: plots/323dfcbe3.svg. 
(1.1.1.3.3.2.2.2.2.2.1) Figure 131. Abundance. Data grouped by Sample.type,visit. violin plot. Image file: plots/32366afa571.svg. 
(1.1.1.3.3.2.2.2.2.2.1) Figure 132. Abundance. Data grouped by Sample.type,visit. boxplot plot. Image file: plots/323aff79f0.svg. 
The same data are shown in multiple combinations of graphical representations. This is the same data, but each plot highlights slightly different aspects of it. It is not likely that you will need every plot - pick only what you need.
(1.1.1.3.3.2.4.2.1.1.0) Table 39. Data table used for plots. Data grouped by Sample.type.Drug.Before,visit. Showing only 200 first rows. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.3.3.2.4.2.1.1.0-323727cf321.1.1.1.3.3.2.4.2.1.1.csv
| .record.id | Sample.type.Drug.Before | visit | feature | Abundance |
|---|---|---|---|---|
| SM1 | patient TRUE . | 1 | Bacteroides | 7.735e-01 |
| SM10 | patient TRUE . | 3 | Bacteroides | 2.364e-01 |
| SM100 | patient TRUE . | 4 | Bacteroides | 5.420e-01 |
| SM11 | patient TRUE . | 2 | Bacteroides | 8.578e-01 |
| SM12 | patient TRUE . | 1 | Bacteroides | 8.674e-01 |
| SM13 | patient FALSE . | 1 | Bacteroides | 4.295e-01 |
| SM14 | patient FALSE . | 1 | Bacteroides | 3.976e-02 |
| SM15 | 1 | 1 | Bacteroides | 4.120e-01 |
| SM16 | patient FALSE . | 4 | Bacteroides | 3.890e-01 |
| SM17 | patient TRUE . | 1 | Bacteroides | 8.130e-01 |
| SM18 | patient FALSE . | 2 | Bacteroides | 6.537e-01 |
| SM19 | patient FALSE . | 2 | Bacteroides | 2.221e-01 |
| SM2 | patient FALSE . | 1 | Bacteroides | 8.611e-01 |
| SM20 | 1 | 1 | Bacteroides | 3.742e-01 |
| SM21 | patient FALSE . | 1 | Bacteroides | 4.490e-01 |
| SM22 | patient TRUE . | 1 | Bacteroides | 5.831e-01 |
| SM23 | patient TRUE . | 2 | Bacteroides | 2.796e-01 |
| SM24 | patient FALSE . | 1 | Bacteroides | 1.435e-01 |
| SM25 | patient FALSE . | 4 | Bacteroides | 4.520e-01 |
| SM26 | 1 | 1 | Bacteroides | 5.242e-01 |
| SM28 | 1 | 1 | Bacteroides | 2.194e-01 |
| SM29 | patient TRUE . | 3 | Bacteroides | 9.002e-01 |
| SM3 | patient TRUE . | 2 | Bacteroides | 2.542e-01 |
| SM30 | patient TRUE . | 4 | Bacteroides | 6.581e-02 |
| SM31 | 1 | 2 | Bacteroides | 4.094e-01 |
| SM33 | patient TRUE . | 1 | Bacteroides | 1.747e-01 |
| SM35 | 1 | 1 | Bacteroides | 6.247e-01 |
| SM36 | patient FALSE . | 4 | Bacteroides | 3.219e-04 |
| SM37 | 1 | 1 | Bacteroides | 3.301e-01 |
| SM38 | patient TRUE . | 2 | Bacteroides | 9.828e-01 |
| SM39 | patient FALSE . | 1 | Bacteroides | 4.095e-01 |
| SM40 | patient FALSE . | 4 | Bacteroides | 6.908e-01 |
| SM41 | patient TRUE . | 1 | Bacteroides | 5.037e-01 |
| SM42 | patient FALSE . | 4 | Bacteroides | 6.901e-01 |
| SM43 | patient TRUE . | 4 | Bacteroides | 6.589e-01 |
| SM44 | 1 | 1 | Bacteroides | 1.150e-02 |
| SM45 | patient FALSE . | 2 | Bacteroides | 0.000e+00 |
| SM48 | 1 | 1 | Bacteroides | 3.247e-01 |
| SM49 | patient TRUE . | 1 | Bacteroides | 9.292e-01 |
| SM5 | patient TRUE . | 3 | Bacteroides | 5.313e-01 |
| SM50 | patient FALSE . | 3 | Bacteroides | 0.000e+00 |
| SM51 | patient TRUE . | 4 | Bacteroides | 7.122e-01 |
| SM52 | patient FALSE . | 1 | Bacteroides | 8.105e-02 |
| SM53 | patient TRUE . | 2 | Bacteroides | 3.305e-01 |
| SM54 | patient TRUE . | 3 | Bacteroides | 6.239e-01 |
| SM55 | 1 | 1 | Bacteroides | 7.465e-02 |
| SM56 | patient TRUE . | 2 | Bacteroides | 1.958e-02 |
| SM57 | patient TRUE . | 1 | Bacteroides | 8.679e-01 |
| SM58 | patient FALSE . | 2 | Bacteroides | 2.592e-02 |
| SM59 | patient FALSE . | 3 | Bacteroides | 5.206e-02 |
| SM60 | patient TRUE . | 3 | Bacteroides | 8.428e-01 |
| SM62 | patient TRUE . | 1 | Bacteroides | 9.643e-01 |
| SM63 | 1 | 1 | Bacteroides | 5.135e-01 |
| SM64 | patient TRUE . | 2 | Bacteroides | 6.977e-01 |
| SM65 | patient TRUE . | 3 | Bacteroides | 3.711e-01 |
| SM66 | 1 | 1 | Bacteroides | 6.218e-01 |
| SM67 | patient TRUE . | 4 | Bacteroides | 5.778e-01 |
| SM68 | patient FALSE . | 4 | Bacteroides | 1.440e-01 |
| SM69 | patient TRUE . | 4 | Bacteroides | 8.051e-01 |
| SM7 | 1 | 1 | Bacteroides | 2.126e-01 |
| SM70 | 1 | 1 | Bacteroides | 6.327e-02 |
| SM71 | patient TRUE . | 3 | Bacteroides | 8.388e-01 |
| SM72 | 1 | 1 | Bacteroides | 4.762e-03 |
| SM73 | patient FALSE . | 1 | Bacteroides | 8.108e-01 |
| SM74 | 1 | 2 | Bacteroides | 8.216e-02 |
| SM75 | patient FALSE . | 3 | Bacteroides | 2.377e-03 |
| SM76 | 1 | 1 | Bacteroides | 8.153e-01 |
| SM77 | patient TRUE . | 2 | Bacteroides | 7.039e-01 |
| SM79 | patient FALSE . | 2 | Bacteroides | 1.173e-01 |
| SM8 | patient FALSE . | 1 | Bacteroides | 7.723e-01 |
| SM81 | 1 | 1 | Bacteroides | 0.000e+00 |
| SM82 | patient TRUE . | 4 | Bacteroides | 8.624e-01 |
| SM83 | patient TRUE . | 1 | Bacteroides | 8.199e-01 |
| SM84 | patient TRUE . | 1 | Bacteroides | 2.885e-01 |
| SM86 | patient TRUE . | 2 | Bacteroides | 2.482e-03 |
| SM87 | patient TRUE . | 1 | Bacteroides | 5.438e-01 |
| SM88 | patient TRUE . | 2 | Bacteroides | 7.940e-01 |
| SM89 | 1 | 1 | Bacteroides | 2.115e-03 |
| SM9 | patient FALSE . | 2 | Bacteroides | 6.096e-01 |
| SM90 | patient FALSE . | 2 | Bacteroides | 4.088e-01 |
| SM91 | patient TRUE . | 3 | Bacteroides | 6.525e-01 |
| SM92 | patient FALSE . | 3 | Bacteroides | 7.921e-01 |
| SM93 | patient TRUE . | 1 | Bacteroides | 6.404e-01 |
| SM95 | 1 | 1 | Bacteroides | 4.955e-01 |
| SM96 | patient FALSE . | 1 | Bacteroides | 6.375e-01 |
| SM98 | patient FALSE . | 3 | Bacteroides | 2.848e-01 |
| SM99 | patient FALSE . | 3 | Bacteroides | 6.503e-01 |
| SM1 | patient TRUE . | 1 | Prevotella | 2.598e-04 |
| SM10 | patient TRUE . | 3 | Prevotella | 0.000e+00 |
| SM100 | patient TRUE . | 4 | Prevotella | 7.692e-05 |
| SM11 | patient TRUE . | 2 | Prevotella | 3.477e-04 |
| SM12 | patient TRUE . | 1 | Prevotella | 1.328e-04 |
| SM13 | patient FALSE . | 1 | Prevotella | 1.652e-02 |
| SM14 | patient FALSE . | 1 | Prevotella | 1.855e-02 |
| SM15 | 1 | 1 | Prevotella | 1.415e-04 |
| SM16 | patient FALSE . | 4 | Prevotella | 0.000e+00 |
| SM17 | patient TRUE . | 1 | Prevotella | 4.137e-04 |
| SM18 | patient FALSE . | 2 | Prevotella | 3.357e-04 |
| SM19 | patient FALSE . | 2 | Prevotella | 2.314e-03 |
| SM2 | patient FALSE . | 1 | Prevotella | 2.480e-04 |
| SM20 | 1 | 1 | Prevotella | 0.000e+00 |
| SM21 | patient FALSE . | 1 | Prevotella | 0.000e+00 |
| SM22 | patient TRUE . | 1 | Prevotella | 0.000e+00 |
| SM23 | patient TRUE . | 2 | Prevotella | 0.000e+00 |
| SM24 | patient FALSE . | 1 | Prevotella | 6.822e-01 |
| SM25 | patient FALSE . | 4 | Prevotella | 0.000e+00 |
| SM26 | 1 | 1 | Prevotella | 2.758e-04 |
| SM28 | 1 | 1 | Prevotella | 3.997e-04 |
| SM29 | patient TRUE . | 3 | Prevotella | 0.000e+00 |
| SM3 | patient TRUE . | 2 | Prevotella | 4.458e-02 |
| SM30 | patient TRUE . | 4 | Prevotella | 2.762e-03 |
| SM31 | 1 | 2 | Prevotella | 1.618e-03 |
| SM33 | patient TRUE . | 1 | Prevotella | 0.000e+00 |
| SM35 | 1 | 1 | Prevotella | 2.046e-03 |
| SM36 | patient FALSE . | 4 | Prevotella | 0.000e+00 |
| SM37 | 1 | 1 | Prevotella | 7.741e-04 |
| SM38 | patient TRUE . | 2 | Prevotella | 1.028e-04 |
| SM39 | patient FALSE . | 1 | Prevotella | 4.073e-01 |
| SM40 | patient FALSE . | 4 | Prevotella | 2.775e-04 |
| SM41 | patient TRUE . | 1 | Prevotella | 0.000e+00 |
| SM42 | patient FALSE . | 4 | Prevotella | 4.994e-04 |
| SM43 | patient TRUE . | 4 | Prevotella | 7.452e-05 |
| SM44 | 1 | 1 | Prevotella | 3.227e-01 |
| SM45 | patient FALSE . | 2 | Prevotella | 0.000e+00 |
| SM48 | 1 | 1 | Prevotella | 2.151e-03 |
| SM49 | patient TRUE . | 1 | Prevotella | 0.000e+00 |
| SM5 | patient TRUE . | 3 | Prevotella | 5.950e-02 |
| SM50 | patient FALSE . | 3 | Prevotella | 0.000e+00 |
| SM51 | patient TRUE . | 4 | Prevotella | 2.231e-04 |
| SM52 | patient FALSE . | 1 | Prevotella | 8.062e-03 |
| SM53 | patient TRUE . | 2 | Prevotella | 4.611e-01 |
| SM54 | patient TRUE . | 3 | Prevotella | 0.000e+00 |
| SM55 | 1 | 1 | Prevotella | 6.747e-01 |
| SM56 | patient TRUE . | 2 | Prevotella | 0.000e+00 |
| SM57 | patient TRUE . | 1 | Prevotella | 3.600e-04 |
| SM58 | patient FALSE . | 2 | Prevotella | 6.582e-01 |
| SM59 | patient FALSE . | 3 | Prevotella | 0.000e+00 |
| SM60 | patient TRUE . | 3 | Prevotella | 3.404e-04 |
| SM62 | patient TRUE . | 1 | Prevotella | 0.000e+00 |
| SM63 | 1 | 1 | Prevotella | 2.703e-03 |
| SM64 | patient TRUE . | 2 | Prevotella | 1.113e-04 |
| SM65 | patient TRUE . | 3 | Prevotella | 1.374e-04 |
| SM66 | 1 | 1 | Prevotella | 2.198e-04 |
| SM67 | patient TRUE . | 4 | Prevotella | 0.000e+00 |
| SM68 | patient FALSE . | 4 | Prevotella | 2.586e-02 |
| SM69 | patient TRUE . | 4 | Prevotella | 3.108e-04 |
| SM7 | 1 | 1 | Prevotella | 0.000e+00 |
| SM70 | 1 | 1 | Prevotella | 4.438e-01 |
| SM71 | patient TRUE . | 3 | Prevotella | 1.723e-03 |
| SM72 | 1 | 1 | Prevotella | 2.651e-01 |
| SM73 | patient FALSE . | 1 | Prevotella | 1.009e-04 |
| SM74 | 1 | 2 | Prevotella | 6.547e-04 |
| SM75 | patient FALSE . | 3 | Prevotella | 0.000e+00 |
| SM76 | 1 | 1 | Prevotella | 5.743e-05 |
| SM77 | patient TRUE . | 2 | Prevotella | 1.127e-04 |
| SM79 | patient FALSE . | 2 | Prevotella | 6.782e-01 |
| SM8 | patient FALSE . | 1 | Prevotella | 7.416e-04 |
| SM81 | 1 | 1 | Prevotella | 0.000e+00 |
| SM82 | patient TRUE . | 4 | Prevotella | 2.141e-04 |
| SM83 | patient TRUE . | 1 | Prevotella | 0.000e+00 |
| SM84 | patient TRUE . | 1 | Prevotella | 4.502e-01 |
| SM86 | patient TRUE . | 2 | Prevotella | 3.103e-04 |
| SM87 | patient TRUE . | 1 | Prevotella | 1.804e-01 |
| SM88 | patient TRUE . | 2 | Prevotella | 1.705e-04 |
| SM89 | 1 | 1 | Prevotella | 8.603e-01 |
| SM9 | patient FALSE . | 2 | Prevotella | 8.227e-04 |
| SM90 | patient FALSE . | 2 | Prevotella | 5.776e-03 |
| SM91 | patient TRUE . | 3 | Prevotella | 2.212e-04 |
| SM92 | patient FALSE . | 3 | Prevotella | 9.411e-02 |
| SM93 | patient TRUE . | 1 | Prevotella | 0.000e+00 |
| SM95 | 1 | 1 | Prevotella | 0.000e+00 |
| SM96 | patient FALSE . | 1 | Prevotella | 0.000e+00 |
| SM98 | patient FALSE . | 3 | Prevotella | 5.140e-01 |
| SM99 | patient FALSE . | 3 | Prevotella | 4.757e-04 |
| SM1 | patient TRUE . | 1 | Unclassified_Lachnospiraceae | 4.529e-02 |
| SM10 | patient TRUE . | 3 | Unclassified_Lachnospiraceae | 2.607e-01 |
| SM100 | patient TRUE . | 4 | Unclassified_Lachnospiraceae | 1.308e-01 |
| SM11 | patient TRUE . | 2 | Unclassified_Lachnospiraceae | 4.404e-03 |
| SM12 | patient TRUE . | 1 | Unclassified_Lachnospiraceae | 1.049e-02 |
| SM13 | patient FALSE . | 1 | Unclassified_Lachnospiraceae | 1.116e-02 |
| SM14 | patient FALSE . | 1 | Unclassified_Lachnospiraceae | 6.172e-02 |
| SM15 | 1 | 1 | Unclassified_Lachnospiraceae | 5.053e-02 |
| SM16 | patient FALSE . | 4 | Unclassified_Lachnospiraceae | 1.583e-01 |
| SM17 | patient TRUE . | 1 | Unclassified_Lachnospiraceae | 2.938e-02 |
| SM18 | patient FALSE . | 2 | Unclassified_Lachnospiraceae | 5.271e-02 |
| SM19 | patient FALSE . | 2 | Unclassified_Lachnospiraceae | 1.055e-01 |
| SM2 | patient FALSE . | 1 | Unclassified_Lachnospiraceae | 1.097e-02 |
| SM20 | 1 | 1 | Unclassified_Lachnospiraceae | 2.256e-02 |
| SM21 | patient FALSE . | 1 | Unclassified_Lachnospiraceae | 5.532e-02 |
| SM22 | patient TRUE . | 1 | Unclassified_Lachnospiraceae | 1.113e-01 |
| SM23 | patient TRUE . | 2 | Unclassified_Lachnospiraceae | 4.148e-04 |
| SM24 | patient FALSE . | 1 | Unclassified_Lachnospiraceae | 1.402e-02 |
| SM25 | patient FALSE . | 4 | Unclassified_Lachnospiraceae | 8.430e-02 |
| SM26 | 1 | 1 | Unclassified_Lachnospiraceae | 7.501e-02 |
| SM28 | 1 | 1 | Unclassified_Lachnospiraceae | 9.952e-02 |
| SM29 | patient TRUE . | 3 | Unclassified_Lachnospiraceae | 1.128e-02 |
| SM3 | patient TRUE . | 2 | Unclassified_Lachnospiraceae | 1.560e-01 |
| SM30 | patient TRUE . | 4 | Unclassified_Lachnospiraceae | 3.297e-01 |
| SM31 | 1 | 2 | Unclassified_Lachnospiraceae | 1.294e-02 |
| SM33 | patient TRUE . | 1 | Unclassified_Lachnospiraceae | 3.934e-03 |
(1.1.1.3.3.2.4.2.1.1.1) Widget 40. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Stacked Bar Chart. Data grouped by Sample.type.Drug.Before,visit. Click to see HTML widget file in full window: ./1.1.1.3.3.2.4.2.1.1.1-32337e0ae4dDynamic.Pivot.Table.html
(1.1.1.3.3.2.4.2.1.1.1) Widget 41. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Table Barchart. Data grouped by Sample.type.Drug.Before,visit. Click to see HTML widget file in full window: ./1.1.1.3.3.2.4.2.1.1.1-3233347c35dDynamic.Pivot.Table.html
(1.1.1.3.3.2.4.2.1.1.1) Table 40. Summary table. Data grouped by Sample.type.Drug.Before,visit. Showing only 200 first rows. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.3.3.2.4.2.1.1.1-3233e9c8a68.1.1.1.3.3.2.4.2.1.1.csv
| feature | Sample.type.Drug.Before | visit | mean | sd | median | incidence |
|---|---|---|---|---|---|---|
| Bacteroides | 1 | 1 | 3.125e-01 | 2.538e-01 | 3.274e-01 | 0.94444 |
| Bacteroides | 1 | 2 | 2.458e-01 | 2.314e-01 | 2.458e-01 | 1.00000 |
| Bacteroides | patient FALSE . | 1 | 4.634e-01 | 3.049e-01 | 4.392e-01 | 1.00000 |
| Bacteroides | patient FALSE . | 2 | 2.911e-01 | 2.698e-01 | 2.221e-01 | 0.85714 |
| Bacteroides | patient FALSE . | 3 | 2.969e-01 | 3.479e-01 | 1.684e-01 | 0.83333 |
| Bacteroides | patient FALSE . | 4 | 3.944e-01 | 2.816e-01 | 4.205e-01 | 1.00000 |
| Bacteroides | patient TRUE . | 1 | 6.746e-01 | 2.463e-01 | 7.735e-01 | 1.00000 |
| Bacteroides | patient TRUE . | 2 | 4.923e-01 | 3.565e-01 | 5.141e-01 | 1.00000 |
| Bacteroides | patient TRUE . | 3 | 6.246e-01 | 2.372e-01 | 6.382e-01 | 1.00000 |
| Bacteroides | patient TRUE . | 4 | 6.035e-01 | 2.634e-01 | 6.589e-01 | 1.00000 |
| Prevotella | 1 | 1 | 1.431e-01 | 2.655e-01 | 5.869e-04 | 0.77778 |
| Prevotella | 1 | 2 | 1.136e-03 | 6.813e-04 | 1.136e-03 | 1.00000 |
| Prevotella | patient FALSE . | 1 | 1.134e-01 | 2.365e-01 | 4.402e-03 | 0.80000 |
| Prevotella | patient FALSE . | 2 | 1.922e-01 | 3.252e-01 | 2.314e-03 | 0.85714 |
| Prevotella | patient FALSE . | 3 | 1.014e-01 | 2.056e-01 | 2.378e-04 | 0.50000 |
| Prevotella | patient FALSE . | 4 | 4.440e-03 | 1.050e-02 | 1.387e-04 | 0.50000 |
| Prevotella | patient TRUE . | 1 | 4.860e-02 | 1.305e-01 | 0.000e+00 | 0.46154 |
| Prevotella | patient TRUE . | 2 | 5.068e-02 | 1.449e-01 | 1.416e-04 | 0.80000 |
| Prevotella | patient TRUE . | 3 | 7.740e-03 | 2.092e-02 | 1.793e-04 | 0.62500 |
| Prevotella | patient TRUE . | 4 | 5.231e-04 | 9.932e-04 | 2.141e-04 | 0.85714 |
| Unclassified_Lachnospiraceae | 1 | 1 | 6.389e-02 | 4.120e-02 | 6.129e-02 | 1.00000 |
| Unclassified_Lachnospiraceae | 1 | 2 | 6.654e-02 | 7.579e-02 | 6.654e-02 | 1.00000 |
| Unclassified_Lachnospiraceae | patient FALSE . | 1 | 3.276e-02 | 3.113e-02 | 1.269e-02 | 1.00000 |
| Unclassified_Lachnospiraceae | patient FALSE . | 2 | 3.552e-02 | 3.529e-02 | 2.075e-02 | 0.85714 |
| Unclassified_Lachnospiraceae | patient FALSE . | 3 | 1.344e-01 | 1.575e-01 | 4.278e-02 | 1.00000 |
| Unclassified_Lachnospiraceae | patient FALSE . | 4 | 9.198e-02 | 4.009e-02 | 9.333e-02 | 1.00000 |
| Unclassified_Lachnospiraceae | patient TRUE . | 1 | 2.669e-02 | 3.274e-02 | 1.049e-02 | 0.92308 |
| Unclassified_Lachnospiraceae | patient TRUE . | 2 | 5.630e-02 | 7.384e-02 | 3.288e-02 | 1.00000 |
| Unclassified_Lachnospiraceae | patient TRUE . | 3 | 7.323e-02 | 8.946e-02 | 3.982e-02 | 1.00000 |
| Unclassified_Lachnospiraceae | patient TRUE . | 4 | 8.273e-02 | 1.170e-01 | 3.912e-02 | 1.00000 |
| Faecalibacterium | 1 | 1 | 4.217e-02 | 4.401e-02 | 3.575e-02 | 0.94444 |
| Faecalibacterium | 1 | 2 | 3.452e-02 | 4.423e-02 | 3.452e-02 | 1.00000 |
| Faecalibacterium | patient FALSE . | 1 | 3.876e-02 | 4.038e-02 | 2.495e-02 | 1.00000 |
| Faecalibacterium | patient FALSE . | 2 | 7.169e-02 | 1.285e-01 | 1.664e-02 | 0.85714 |
| Faecalibacterium | patient FALSE . | 3 | 2.433e-02 | 2.073e-02 | 1.749e-02 | 1.00000 |
| Faecalibacterium | patient FALSE . | 4 | 9.878e-02 | 9.939e-02 | 6.677e-02 | 1.00000 |
| Faecalibacterium | patient TRUE . | 1 | 1.846e-02 | 1.438e-02 | 1.267e-02 | 0.92308 |
| Faecalibacterium | patient TRUE . | 2 | 5.171e-02 | 1.083e-01 | 1.129e-02 | 0.90000 |
| Faecalibacterium | patient TRUE . | 3 | 4.364e-02 | 4.948e-02 | 2.507e-02 | 1.00000 |
| Faecalibacterium | patient TRUE . | 4 | 3.871e-02 | 4.144e-02 | 1.950e-02 | 1.00000 |
| Lachnospiracea_incertae_sedis | 1 | 1 | 3.238e-02 | 2.664e-02 | 2.788e-02 | 0.94444 |
| Lachnospiracea_incertae_sedis | 1 | 2 | 5.683e-02 | 7.980e-02 | 5.683e-02 | 1.00000 |
| Lachnospiracea_incertae_sedis | patient FALSE . | 1 | 9.291e-03 | 8.958e-03 | 6.378e-03 | 1.00000 |
| Lachnospiracea_incertae_sedis | patient FALSE . | 2 | 1.942e-02 | 1.950e-02 | 1.145e-02 | 0.85714 |
| Lachnospiracea_incertae_sedis | patient FALSE . | 3 | 7.174e-02 | 1.013e-01 | 1.093e-02 | 1.00000 |
| Lachnospiracea_incertae_sedis | patient FALSE . | 4 | 8.868e-02 | 6.950e-02 | 7.666e-02 | 1.00000 |
| Lachnospiracea_incertae_sedis | patient TRUE . | 1 | 1.085e-02 | 1.317e-02 | 3.240e-03 | 0.84615 |
| Lachnospiracea_incertae_sedis | patient TRUE . | 2 | 4.535e-02 | 5.535e-02 | 2.253e-02 | 0.90000 |
| Lachnospiracea_incertae_sedis | patient TRUE . | 3 | 4.177e-02 | 4.937e-02 | 2.248e-02 | 0.87500 |
| Lachnospiracea_incertae_sedis | patient TRUE . | 4 | 2.672e-02 | 3.288e-02 | 1.450e-02 | 0.85714 |
| Parabacteroides | 1 | 1 | 8.828e-03 | 8.069e-03 | 6.610e-03 | 0.94444 |
| Parabacteroides | 1 | 2 | 1.807e-02 | 1.907e-02 | 1.807e-02 | 1.00000 |
| Parabacteroides | patient FALSE . | 1 | 1.024e-02 | 1.289e-02 | 2.166e-03 | 0.80000 |
| Parabacteroides | patient FALSE . | 2 | 2.816e-02 | 5.131e-02 | 1.370e-03 | 0.85714 |
| Parabacteroides | patient FALSE . | 3 | 8.124e-03 | 1.641e-02 | 0.000e+00 | 0.33333 |
| Parabacteroides | patient FALSE . | 4 | 2.621e-03 | 5.406e-03 | 1.849e-04 | 0.66667 |
| Parabacteroides | patient TRUE . | 1 | 5.820e-02 | 1.381e-01 | 7.199e-03 | 0.69231 |
| Parabacteroides | patient TRUE . | 2 | 7.576e-02 | 2.222e-01 | 5.432e-04 | 0.80000 |
| Parabacteroides | patient TRUE . | 3 | 5.231e-02 | 7.215e-02 | 1.782e-02 | 0.87500 |
| Parabacteroides | patient TRUE . | 4 | 6.228e-02 | 1.228e-01 | 2.231e-04 | 0.71429 |
| Alistipes | 1 | 1 | 4.359e-02 | 7.436e-02 | 1.748e-02 | 0.77778 |
| Alistipes | 1 | 2 | 6.305e-02 | 8.361e-02 | 6.305e-02 | 1.00000 |
| Alistipes | patient FALSE . | 1 | 5.269e-02 | 7.947e-02 | 1.928e-02 | 0.70000 |
| Alistipes | patient FALSE . | 2 | 1.185e-02 | 1.874e-02 | 6.851e-04 | 0.57143 |
| Alistipes | patient FALSE . | 3 | 8.739e-04 | 2.141e-03 | 0.000e+00 | 0.16667 |
| Alistipes | patient FALSE . | 4 | 4.068e-03 | 8.729e-03 | 4.160e-04 | 0.50000 |
| Alistipes | patient TRUE . | 1 | 1.696e-02 | 2.078e-02 | 9.784e-03 | 0.69231 |
| Alistipes | patient TRUE . | 2 | 2.759e-02 | 5.265e-02 | 0.000e+00 | 0.40000 |
| Alistipes | patient TRUE . | 3 | 1.056e-02 | 2.049e-02 | 1.516e-03 | 0.62500 |
| Alistipes | patient TRUE . | 4 | 9.648e-03 | 1.404e-02 | 2.660e-03 | 0.57143 |
| Blautia | 1 | 1 | 2.657e-02 | 4.449e-02 | 1.644e-02 | 1.00000 |
| Blautia | 1 | 2 | 4.533e-02 | 6.181e-02 | 4.533e-02 | 1.00000 |
| Blautia | patient FALSE . | 1 | 1.828e-02 | 2.097e-02 | 5.935e-03 | 1.00000 |
| Blautia | patient FALSE . | 2 | 1.872e-02 | 3.047e-02 | 2.936e-03 | 0.85714 |
| Blautia | patient FALSE . | 3 | 3.677e-02 | 3.608e-02 | 2.566e-02 | 1.00000 |
| Blautia | patient FALSE . | 4 | 1.189e-02 | 8.838e-03 | 8.247e-03 | 1.00000 |
| Blautia | patient TRUE . | 1 | 7.798e-03 | 1.057e-02 | 3.143e-03 | 0.92308 |
| Blautia | patient TRUE . | 2 | 1.865e-02 | 3.688e-02 | 8.351e-03 | 0.80000 |
| Blautia | patient TRUE . | 3 | 1.381e-02 | 1.440e-02 | 9.423e-03 | 1.00000 |
| Blautia | patient TRUE . | 4 | 1.700e-02 | 2.588e-02 | 6.334e-03 | 1.00000 |
| Ruminococcus | 1 | 1 | 5.576e-02 | 8.722e-02 | 2.428e-02 | 0.94444 |
| Ruminococcus | 1 | 2 | 1.140e-01 | 1.424e-01 | 1.140e-01 | 1.00000 |
| Ruminococcus | patient FALSE . | 1 | 4.312e-03 | 4.547e-03 | 2.962e-03 | 1.00000 |
| Ruminococcus | patient FALSE . | 2 | 8.027e-03 | 1.303e-02 | 1.175e-03 | 0.57143 |
| Ruminococcus | patient FALSE . | 3 | 2.267e-02 | 3.043e-02 | 1.710e-02 | 1.00000 |
| Ruminococcus | patient FALSE . | 4 | 1.248e-02 | 1.947e-02 | 2.719e-03 | 0.66667 |
| Ruminococcus | patient TRUE . | 1 | 5.840e-03 | 1.170e-02 | 1.647e-03 | 0.84615 |
| Ruminococcus | patient TRUE . | 2 | 2.893e-03 | 2.465e-03 | 2.473e-03 | 0.90000 |
| Ruminococcus | patient TRUE . | 3 | 2.368e-03 | 2.385e-03 | 1.529e-03 | 0.75000 |
| Ruminococcus | patient TRUE . | 4 | 1.994e-03 | 2.008e-03 | 1.988e-03 | 0.85714 |
| Unclassified_Clostridiales | 1 | 1 | 1.825e-02 | 2.169e-02 | 1.279e-02 | 0.94444 |
| Unclassified_Clostridiales | 1 | 2 | 3.991e-02 | 2.040e-02 | 3.991e-02 | 1.00000 |
| Unclassified_Clostridiales | patient FALSE . | 1 | 1.711e-02 | 1.800e-02 | 8.182e-03 | 1.00000 |
| Unclassified_Clostridiales | patient FALSE . | 2 | 1.125e-02 | 1.229e-02 | 8.058e-03 | 0.85714 |
| Unclassified_Clostridiales | patient FALSE . | 3 | 5.322e-02 | 9.895e-02 | 1.471e-02 | 1.00000 |
| Unclassified_Clostridiales | patient FALSE . | 4 | 2.119e-02 | 2.066e-02 | 1.448e-02 | 1.00000 |
| Unclassified_Clostridiales | patient TRUE . | 1 | 6.632e-03 | 8.900e-03 | 6.030e-03 | 1.00000 |
| Unclassified_Clostridiales | patient TRUE . | 2 | 8.688e-03 | 1.226e-02 | 4.161e-03 | 0.90000 |
| Unclassified_Clostridiales | patient TRUE . | 3 | 1.341e-02 | 1.283e-02 | 9.805e-03 | 1.00000 |
| Unclassified_Clostridiales | patient TRUE . | 4 | 6.315e-03 | 5.937e-03 | 5.354e-03 | 1.00000 |
| Lactobacillus | 1 | 1 | 1.522e-02 | 6.414e-02 | 0.000e+00 | 0.27778 |
| Lactobacillus | 1 | 2 | 0.000e+00 | 0.000e+00 | 0.000e+00 | 0.00000 |
| Lactobacillus | patient FALSE . | 1 | 8.034e-04 | 1.696e-03 | 0.000e+00 | 0.40000 |
| Lactobacillus | patient FALSE . | 2 | 1.426e-01 | 3.768e-01 | 0.000e+00 | 0.28571 |
| Lactobacillus | patient FALSE . | 3 | 8.881e-04 | 1.905e-03 | 2.458e-05 | 0.50000 |
| Lactobacillus | patient FALSE . | 4 | 1.086e-03 | 2.200e-03 | 1.609e-04 | 0.50000 |
| Lactobacillus | patient TRUE . | 1 | 0.000e+00 | 0.000e+00 | 0.000e+00 | 0.00000 |
| Lactobacillus | patient TRUE . | 2 | 1.384e-04 | 3.240e-04 | 0.000e+00 | 0.30000 |
| Lactobacillus | patient TRUE . | 3 | 0.000e+00 | 0.000e+00 | 0.000e+00 | 0.00000 |
| Lactobacillus | patient TRUE . | 4 | 0.000e+00 | 0.000e+00 | 0.000e+00 | 0.00000 |
| Unclassified_Ruminococcaceae | 1 | 1 | 3.224e-02 | 3.357e-02 | 1.940e-02 | 0.94444 |
| Unclassified_Ruminococcaceae | 1 | 2 | 5.710e-02 | 4.511e-02 | 5.710e-02 | 1.00000 |
| Unclassified_Ruminococcaceae | patient FALSE . | 1 | 1.774e-02 | 3.797e-02 | 5.337e-03 | 1.00000 |
| Unclassified_Ruminococcaceae | patient FALSE . | 2 | 8.976e-03 | 1.262e-02 | 3.861e-03 | 0.85714 |
| Unclassified_Ruminococcaceae | patient FALSE . | 3 | 8.313e-03 | 1.001e-02 | 4.539e-03 | 1.00000 |
| Unclassified_Ruminococcaceae | patient FALSE . | 4 | 1.269e-02 | 1.408e-02 | 7.225e-03 | 1.00000 |
| Unclassified_Ruminococcaceae | patient TRUE . | 1 | 8.291e-03 | 7.539e-03 | 6.698e-03 | 1.00000 |
| Unclassified_Ruminococcaceae | patient TRUE . | 2 | 3.945e-03 | 3.629e-03 | 2.494e-03 | 0.90000 |
| Unclassified_Ruminococcaceae | patient TRUE . | 3 | 4.088e-03 | 5.283e-03 | 2.960e-03 | 1.00000 |
| Unclassified_Ruminococcaceae | patient TRUE . | 4 | 5.241e-03 | 9.406e-03 | 2.293e-03 | 1.00000 |
| Roseburia | 1 | 1 | 9.054e-03 | 6.994e-03 | 6.302e-03 | 1.00000 |
| Roseburia | 1 | 2 | 1.069e-02 | 7.105e-03 | 1.069e-02 | 1.00000 |
| Roseburia | patient FALSE . | 1 | 7.028e-03 | 7.428e-03 | 3.183e-03 | 1.00000 |
| Roseburia | patient FALSE . | 2 | 1.860e-02 | 3.406e-02 | 3.861e-03 | 0.85714 |
| Roseburia | patient FALSE . | 3 | 1.395e-02 | 1.660e-02 | 9.751e-03 | 1.00000 |
| Roseburia | patient FALSE . | 4 | 5.491e-02 | 4.492e-02 | 5.431e-02 | 1.00000 |
| Roseburia | patient TRUE . | 1 | 3.915e-03 | 5.016e-03 | 2.110e-03 | 0.76923 |
| Roseburia | patient TRUE . | 2 | 1.514e-02 | 1.970e-02 | 6.342e-03 | 1.00000 |
| Roseburia | patient TRUE . | 3 | 1.537e-02 | 1.691e-02 | 1.115e-02 | 1.00000 |
| Roseburia | patient TRUE . | 4 | 2.036e-02 | 2.166e-02 | 2.208e-02 | 1.00000 |
| Clostridium_XI | 1 | 1 | 9.259e-03 | 1.086e-02 | 6.425e-03 | 0.94444 |
| Clostridium_XI | 1 | 2 | 1.387e-02 | 8.167e-03 | 1.387e-02 | 1.00000 |
| Clostridium_XI | patient FALSE . | 1 | 3.278e-02 | 6.673e-02 | 3.583e-03 | 0.90000 |
| Clostridium_XI | patient FALSE . | 2 | 4.192e-03 | 6.009e-03 | 2.854e-03 | 0.57143 |
| Clostridium_XI | patient FALSE . | 3 | 4.168e-03 | 5.149e-03 | 2.607e-03 | 0.83333 |
| Clostridium_XI | patient FALSE . | 4 | 3.122e-02 | 4.815e-02 | 1.455e-02 | 1.00000 |
| Clostridium_XI | patient TRUE . | 1 | 5.585e-03 | 1.194e-02 | 1.655e-03 | 0.76923 |
| Clostridium_XI | patient TRUE . | 2 | 1.709e-02 | 4.566e-02 | 1.260e-03 | 0.90000 |
| Clostridium_XI | patient TRUE . | 3 | 8.726e-03 | 1.128e-02 | 2.379e-03 | 1.00000 |
| Clostridium_XI | patient TRUE . | 4 | 1.728e-02 | 2.154e-02 | 5.589e-03 | 1.00000 |
| Enterococcus | 1 | 1 | 3.133e-03 | 1.317e-02 | 0.000e+00 | 0.16667 |
| Enterococcus | 1 | 2 | 3.437e-03 | 4.861e-03 | 3.437e-03 | 0.50000 |
| Enterococcus | patient FALSE . | 1 | 7.389e-03 | 2.263e-02 | 5.447e-05 | 0.50000 |
| Enterococcus | patient FALSE . | 2 | 4.235e-04 | 6.395e-04 | 0.000e+00 | 0.42857 |
| Enterococcus | patient FALSE . | 3 | 3.121e-04 | 7.645e-04 | 0.000e+00 | 0.16667 |
| Enterococcus | patient FALSE . | 4 | 5.194e-05 | 1.272e-04 | 0.000e+00 | 0.16667 |
| Enterococcus | patient TRUE . | 1 | 3.162e-04 | 9.135e-04 | 0.000e+00 | 0.23077 |
| Enterococcus | patient TRUE . | 2 | 7.148e-02 | 2.245e-01 | 0.000e+00 | 0.40000 |
| Enterococcus | patient TRUE . | 3 | 2.586e-04 | 4.652e-04 | 0.000e+00 | 0.37500 |
| Enterococcus | patient TRUE . | 4 | 5.191e-04 | 9.098e-04 | 0.000e+00 | 0.28571 |
| Erysipelotrichaceae_incertae_sedis | 1 | 1 | 1.177e-03 | 1.604e-03 | 6.149e-04 | 0.77778 |
| Erysipelotrichaceae_incertae_sedis | 1 | 2 | 8.955e-04 | 1.223e-04 | 8.955e-04 | 1.00000 |
| Erysipelotrichaceae_incertae_sedis | patient FALSE . | 1 | 4.282e-02 | 1.209e-01 | 1.055e-03 | 0.80000 |
| Erysipelotrichaceae_incertae_sedis | patient FALSE . | 2 | 1.497e-03 | 2.797e-03 | 1.957e-04 | 0.57143 |
| Erysipelotrichaceae_incertae_sedis | patient FALSE . | 3 | 1.465e-02 | 1.880e-02 | 6.028e-03 | 1.00000 |
| Erysipelotrichaceae_incertae_sedis | patient FALSE . | 4 | 3.076e-02 | 7.402e-02 | 2.127e-04 | 0.66667 |
| Erysipelotrichaceae_incertae_sedis | patient TRUE . | 1 | 2.576e-03 | 3.115e-03 | 1.373e-03 | 0.69231 |
| Erysipelotrichaceae_incertae_sedis | patient TRUE . | 2 | 1.907e-03 | 3.034e-03 | 5.660e-04 | 1.00000 |
| Erysipelotrichaceae_incertae_sedis | patient TRUE . | 3 | 5.662e-03 | 8.182e-03 | 2.557e-03 | 1.00000 |
| Erysipelotrichaceae_incertae_sedis | patient TRUE . | 4 | 1.908e-03 | 1.198e-03 | 2.231e-03 | 1.00000 |
| Megamonas | 1 | 1 | 1.856e-02 | 5.287e-02 | 0.000e+00 | 0.16667 |
| Megamonas | 1 | 2 | 0.000e+00 | 0.000e+00 | 0.000e+00 | 0.00000 |
| Megamonas | patient FALSE . | 1 | 1.089e-05 | 3.445e-05 | 0.000e+00 | 0.10000 |
| Megamonas | patient FALSE . | 2 | 4.764e-02 | 8.486e-02 | 0.000e+00 | 0.28571 |
| Megamonas | patient FALSE . | 3 | 6.492e-03 | 1.590e-02 | 0.000e+00 | 0.16667 |
| Megamonas | patient FALSE . | 4 | 4.717e-03 | 1.156e-02 | 0.000e+00 | 0.16667 |
| Megamonas | patient TRUE . | 1 | 3.839e-03 | 1.384e-02 | 0.000e+00 | 0.07692 |
| Megamonas | patient TRUE . | 2 | 0.000e+00 | 0.000e+00 | 0.000e+00 | 0.00000 |
| Megamonas | patient TRUE . | 3 | 0.000e+00 | 0.000e+00 | 0.000e+00 | 0.00000 |
| Megamonas | patient TRUE . | 4 | 2.053e-04 | 5.432e-04 | 0.000e+00 | 0.14286 |
| Sutterella | 1 | 1 | 1.005e-02 | 2.746e-02 | 1.351e-03 | 0.61111 |
| Sutterella | 1 | 2 | 0.000e+00 | 0.000e+00 | 0.000e+00 | 0.00000 |
| Sutterella | patient FALSE . | 1 | 5.495e-03 | 1.166e-02 | 1.302e-04 | 0.70000 |
| Sutterella | patient FALSE . | 2 | 9.702e-03 | 1.627e-02 | 0.000e+00 | 0.42857 |
| Sutterella | patient FALSE . | 3 | 6.242e-05 | 1.529e-04 | 0.000e+00 | 0.16667 |
| Sutterella | patient FALSE . | 4 | 1.555e-02 | 3.337e-02 | 3.219e-04 | 0.50000 |
| Sutterella | patient TRUE . | 1 | 7.355e-03 | 1.737e-02 | 0.000e+00 | 0.38462 |
| Sutterella | patient TRUE . | 2 | 5.365e-03 | 1.176e-02 | 0.000e+00 | 0.20000 |
| Sutterella | patient TRUE . | 3 | 8.784e-03 | 1.627e-02 | 0.000e+00 | 0.25000 |
| Sutterella | patient TRUE . | 4 | 5.578e-03 | 1.476e-02 | 0.000e+00 | 0.14286 |
| Escherichia_Shigella | 1 | 1 | 1.014e-02 | 3.951e-02 | 3.219e-04 | 0.55556 |
| Escherichia_Shigella | 1 | 2 | 4.045e-04 | 5.721e-04 | 4.045e-04 | 0.50000 |
| Escherichia_Shigella | patient FALSE . | 1 | 1.337e-02 | 4.052e-02 | 6.431e-05 | 0.50000 |
| Escherichia_Shigella | patient FALSE . | 2 | 8.508e-04 | 2.001e-03 | 0.000e+00 | 0.42857 |
| Escherichia_Shigella | patient FALSE . | 3 | 1.739e-03 | 1.694e-03 | 1.798e-03 | 0.66667 |
| Escherichia_Shigella | patient FALSE . | 4 | 2.261e-04 | 3.197e-04 | 4.161e-05 | 0.50000 |
| Escherichia_Shigella | patient TRUE . | 1 | 1.466e-02 | 4.824e-02 | 0.000e+00 | 0.30769 |
| Escherichia_Shigella | patient TRUE . | 2 | 1.239e-05 | 2.833e-05 | 0.000e+00 | 0.20000 |
| Escherichia_Shigella | patient TRUE . | 3 | 2.818e-03 | 6.836e-03 | 3.157e-04 | 0.62500 |
| Escherichia_Shigella | patient TRUE . | 4 | 1.381e-02 | 2.232e-02 | 1.590e-03 | 0.57143 |
| Unclassified_Bacteria | 1 | 1 | 1.364e-02 | 1.141e-02 | 1.054e-02 | 1.00000 |
| Unclassified_Bacteria | 1 | 2 | 2.617e-02 | 3.243e-02 | 2.617e-02 | 1.00000 |
| Unclassified_Bacteria | patient FALSE . | 1 | 1.480e-02 | 2.717e-02 | 4.448e-03 | 1.00000 |
| Unclassified_Bacteria | patient FALSE . | 2 | 2.186e-03 | 2.207e-03 | 1.388e-03 | 0.85714 |
| Unclassified_Bacteria | patient FALSE . | 3 | 5.270e-03 | 3.824e-03 | 3.444e-03 | 1.00000 |
| Unclassified_Bacteria | patient FALSE . | 4 | 4.114e-03 | 4.251e-03 | 2.007e-03 | 1.00000 |
| Unclassified_Bacteria | patient TRUE . | 1 | 3.807e-03 | 4.164e-03 | 2.257e-03 | 0.92308 |
| Unclassified_Bacteria | patient TRUE . | 2 | 2.145e-03 | 1.812e-03 | 2.054e-03 | 0.90000 |
| Unclassified_Bacteria | patient TRUE . | 3 | 1.982e-03 | 1.537e-03 | 1.345e-03 | 1.00000 |
| Unclassified_Bacteria | patient TRUE . | 4 | 5.219e-03 | 8.370e-03 | 1.399e-03 | 1.00000 |
(1.1.1.3.3.2.4.2.1.1.1) Figure 133. Abundance. Data grouped by Sample.type.Drug.Before,visit. bar_stacked plot. Image file: plots/3231fb06f76.svg. 
(1.1.1.3.3.2.4.2.1.1.1) Figure 134. Abundance. Data grouped by Sample.type.Drug.Before,visit. bar (sample mean) plot. Image file: plots/323257a115b.svg. 
(1.1.1.3.3.2.4.2.1.1.1) Figure 135. Abundance. Data grouped by Sample.type.Drug.Before,visit. violin plot. Image file: plots/32363bf503d.svg. 
(1.1.1.3.3.2.4.2.1.1.1) Figure 136. Abundance. Data grouped by Sample.type.Drug.Before,visit. boxplot plot. Image file: plots/3233842f76e.svg. 
(1.1.1.3.3.2.4.2.1.2.1) Figure 137. Abundance. Data grouped by Sample.type.Drug.Before,visit. bar (sample mean) plot. Image file: plots/3237e83f6a.svg. 
(1.1.1.3.3.2.4.2.1.2.1) Figure 138. Abundance. Data grouped by Sample.type.Drug.Before,visit. violin plot. Image file: plots/3235acec018.svg. 
(1.1.1.3.3.2.4.2.1.2.1) Figure 139. Abundance. Data grouped by Sample.type.Drug.Before,visit. boxplot plot. Image file: plots/32330bdd2c6.svg. 
